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232,829 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: Gene Name = "nucS"

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Search Summary

This query matches 68 Structures.

Refinements

Structure Determination Methodology

	computational (58)
	experimental (10)

CSM Source Database

AlphaFoldDB (58)

pLDDT Global Quality Score

	70.0 - 90.0 (7)
	> 90.0 (51)

Scientific Name of Source Organism

	Aspergillus oryzae RIB40 (10)
	Cladophialophora carrionii (2)
	Aeropyrum pernix K1 (1)
	Arthrobacter sp. FB24 (1)
	Beutenbergia cavernae DSM 12333 (1)
	Bifidobacterium adolescentis ATCC 15703 (1)
	Bifidobacterium animalis subsp. lactis AD011 (1)
	Bifidobacterium longum DJO10A (1)
	Bifidobacterium longum NCC2705 (1)
	Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088 (1)

More...

Taxonomy

	Bacteria (38)
	Archaea (18)
	Eukaryota (12)

Experimental Method

X-RAY DIFFRACTION (10)

Polymer Entity Type

Protein (68)

Refinement Resolution (Å)

	1.0 - 1.5 (3)
	1.5 - 2.0 (6)
	2.5 - 3.0 (1)

Release Date

	2005 - 2009 (1)
	2015 - 2019 (7)
	2020 - 2024 (60)

Enzyme Classification Name

Hydrolases (66)

Symmetry Type

	Asymmetric (67)
	Cyclic (1)

SCOP Classification

All alpha proteins (7)

AllSelected

1 to 25 of 68 Structures

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2VLD	Download File View File

crystal structure of a repair endonuclease from Pyrococcus abyssi

Ren, B., Kuhn, J., Meslet-Cladiere, L., Briffotaux, J., Norais, C., Lavigne, R., Flament, D., Ladenstein, R., Myllykallio, H.

(2009) EMBO J 28: 2479-2489

Released	2009-05-19
Method	X-RAY DIFFRACTION 2.6 Å
Organisms	Pyrococcus abyssi
Macromolecule	Endonuclease NucS (protein)

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5FB9	Download File View File

S1 nuclease from Aspergillus oryzae with unoccupied active site

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	BTB, NA, NAG, ZN

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5FBA	Download File View File

S1 nuclease from Aspergillus oryzae in complex with phosphate

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	GOL, NAG, PO4, ZN

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5FBB	Download File View File

S1 nuclease from Aspergillus oryzae in complex with phosphate and adenosine 5'-monophosphate

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	AMP, BTB, CA, ETE, NA, NAG, PO4, ZN

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5FBC	Download File View File

S1 nuclease from Aspergillus oryzae in complex with 2'-deoxyadenosine-5'-thio-monophosphate (5'dAMP(S)).

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	AS, GOL, NAG, ZN

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5FBD	Download File View File

S1 nuclease from Aspergillus oryzae in complex with phosphate and 2'-deoxycytidine

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.75 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	DCZ, NAG, PO4, ZN

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5FBF	Download File View File

S1 nuclease from Aspergillus oryzae in complex with two molecules of 2'-deoxycytidine-5'-monophosphate

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.04 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	DCM, NA, NAG, ZN

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5FBG	Download File View File

S1 nuclease from Aspergillus oryzae, mutant D65N, in complex with phosphate, 2'-deoxycytidine and 2'-deoxyguanosine.

Koval, T., Oestergaard, L.H., Dohnalek, J.

(2016) PLoS One 11: e0168832-e0168832

Released	2016-12-28
Method	X-RAY DIFFRACTION 1.97 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	DCZ, GNG, NAG, PO4, ZN

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7QTA	Download File View File

S1 nuclease from Aspergillus oryzae in complex with uridine

Adamkova, K., Koval, T., Kolenko, P., Oestergaard, L.H., Dohnalek, J.

(2022) Acta Crystallogr D Struct Biol 78: 1194-1209

Released	2022-11-09
Method	X-RAY DIFFRACTION 1.06 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	BTB, NA, NAG, PO4, URI, ZN

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7QTB	Download File View File

S1 nuclease from Aspergillus oryzae in complex with cytidine-5'-monophosphate

Adamkova, K., Koval, T., Kolenko, P., Oestergaard, L.H., Dohnalek, J.

(2022) Acta Crystallogr D Struct Biol 78: 1194-1209

Released	2022-11-09
Method	X-RAY DIFFRACTION 1.04 Å
Organisms	Aspergillus oryzae RIB40
Macromolecule	Nuclease S1 (protein)
Unique Ligands	BTB, C5P, CA, NAG, PO4, ZN

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AF_AFA0A1C1CS61F1	Download File

Computed structure model of Nuclease S1

AlphaFold DB	AF-A0A1C1CS61-F1
pLDDT (global)	89.74
Organisms	Cladophialophora carrionii
Macromolecule	Nuclease S1 (protein)

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AF_AFA0A1C1CUF8F1	Download File

Computed structure model of Nuclease S1

AlphaFold DB	AF-A0A1C1CUF8-F1
pLDDT (global)	94.95
Organisms	Cladophialophora carrionii
Macromolecule	Nuclease S1 (protein)

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AF_AFA0JY58F1	Download File

Computed structure model of Endonuclease NucS

AlphaFold DB	AF-A0JY58-F1
pLDDT (global)	93.1
Organisms	Arthrobacter sp. FB24
Macromolecule	Endonuclease NucS (protein)

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AF_AFA0PUJ0F1	Download File

Computed structure model of Endonuclease NucS

AlphaFold DB	AF-A0PUJ0-F1
pLDDT (global)	91.79
Organisms	Mycobacterium ulcerans Agy99
Macromolecule	Endonuclease NucS (protein)

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AF_AFA0R1Z0F1	Download File

Computed structure model of Endonuclease NucS

AlphaFold DB	AF-A0R1Z0-F1
pLDDT (global)	91.94
Organisms	Mycolicibacterium smegmatis MC2 155
Macromolecule	Endonuclease NucS (protein)

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AF_AFA1A3C3F1	Download File

Computed structure model of Endonuclease NucS

AlphaFold DB	AF-A1A3C3-F1
pLDDT (global)	93.41
Organisms	Bifidobacterium adolescentis ATCC 15703
Macromolecule	Endonuclease NucS (protein)

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AF_AFA1TD35F1	Download File

Computed structure model of Endonuclease NucS

AlphaFold DB	AF-A1TD35-F1
pLDDT (global)	92.65
Organisms	Mycolicibacterium vanbaalenii PYR-1
Macromolecule	Endonuclease NucS (protein)

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AF_AFA3Q3A2F1	Download File

Computed structure model of Endonuclease NucS

AlphaFold DB	AF-A3Q3A2-F1
pLDDT (global)	92.6
Organisms	Mycobacterium sp. JLS
Macromolecule	Endonuclease NucS (protein)

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AF_AFA4QDH7F1	Download File

Computed structure model of Endonuclease NucS

AlphaFold DB	AF-A4QDH7-F1
pLDDT (global)	92.55
Organisms	Corynebacterium glutamicum R
Macromolecule	Endonuclease NucS (protein)

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AF_AFA4T8H8F1	Download File

Computed structure model of Endonuclease NucS

AlphaFold DB	AF-A4T8H8-F1
pLDDT (global)	91.78
Organisms	Mycolicibacterium gilvum PYR-GCK
Macromolecule	Endonuclease NucS (protein)

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AF_AFA8L3X7F1	Download File

Computed structure model of Endonuclease NucS

AlphaFold DB	AF-A8L3X7-F1
pLDDT (global)	91.97
Organisms	Parafrankia sp. EAN1pec
Macromolecule	Endonuclease NucS (protein)

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AF_AFB1MLW9F1	Download File

Computed structure model of Endonuclease NucS

AlphaFold DB	AF-B1MLW9-F1
pLDDT (global)	90.73
Organisms	Mycobacteroides abscessus ATCC 19977
Macromolecule	Endonuclease NucS (protein)

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AF_AFB1VFZ0F1	Download File

Computed structure model of Endonuclease NucS

AlphaFold DB	AF-B1VFZ0-F1
pLDDT (global)	91.79
Organisms	Corynebacterium urealyticum DSM 7109
Macromolecule	Endonuclease NucS (protein)

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AF_AFB1W089F1	Download File

Computed structure model of Endonuclease NucS

AlphaFold DB	AF-B1W089-F1
pLDDT (global)	90.91
Organisms	Streptomyces griseus subsp. griseus NBRC 13350
Macromolecule	Endonuclease NucS (protein)

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AF_AFB2GLZ4F1	Download File

Computed structure model of Endonuclease NucS

AlphaFold DB	AF-B2GLZ4-F1
pLDDT (global)	93.62
Organisms	Kocuria rhizophila DC2201
Macromolecule	Endonuclease NucS (protein)

1 to 25 of 68 Structures

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Structure Determination Methodology

CSM Source Database

pLDDT Global Quality Score

Scientific Name of Source Organism

Taxonomy

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Release Date

Enzyme Classification Name

Symmetry Type

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